Molecular Phylogenetics and Historical Biogeography of Basal Angiosperms

227 Pages·2006·6.76 MB·English

by  Cornelia Löhne

Molecular Phylogenetics and Historical Biogeography
of Basal Angiosperms
– A Case Study in Nymphaeales –

Dissertation

zur
Erlangung des Doktorgrades (Dr. rer. nat.)
der
Mathematisch–Naturwissenschaftlichen Fakultät
der Rheinischen Friedrich–Wilhelms–Universität Bonn

vorgelegt von

Cornelia Löhne
aus
Leipzig

Bonn, März 2006

Angefertigt mit Genehmigung der Mathematisch–Naturwissenschaftlichen Fakultät
der Rheinischen Friedrich-Wilhems-Universität Bonn.

Erstgutachter: Prof. Dr. Wilhelm Barthlott
Zweitgutachter: PD Dr. Thomas Borsch

Tag der mündlichen Prüfung: 30.5.2006
Diese Dissertation ist auf dem Hochschulschriftenserver der ULB Bonn
http://hss.ulb.uni-bonn.de/diss_online elektronisch publiziert.
Erscheinungsjahr 2007
II
Preface and Acknowledgements

The present thesis was carried out in the framework of the Graduiertenkolleg “Evolution and
Biodiversity in Time and Space” and supported by a graduate student fellowship from the
Deutsche Forschungsgemeinschaft (DFG–Graduiertenkolleg 721), and supervised by Prof.
Wilhelm Barthlott and Dr. habil. Thomas Borsch.
The Graduiertenkolleg “Evolution and Biodiversity in Time and Space” united researchers
and graduate students from the fields of organismic zoology, botany, developmental biology
as well as palaeontology. In the course of several seminars and workshops all participants
could exchange their specific knowledge and experience in fruitful discussions, broaden
their horizons and get a wider picture on the diversity of organisms and their evolution. This
innovative approach was extremely inspiring and provided a solid basis and backbone for
my own interdisciplinary study.
Many persons have been of great importance for this PhD project. First of all, I would like to
express my gratitude to Prof. Wilhelm Barthlott. He gave me the chance to step into this
integrative field of botany by inviting me to start this PhD project under his supervision in
2002. His stimulating fascination for the diversity of plants, together with his encouragement
and support throughout the years were of great help. Also, I am indebted to Dr. Thomas
Borsch, who introduced me into the world of phylogenetic systematics and molecular
evolution. Without his continuous support and encouragement the present project would not
have been possible. His valuable suggestions and comments on all parts of this thesis as well
as his experience with the water lilies are greatly appreciated.
Furthermore, I would like to express my gratitude to John Wiersema (US Department of
Agriculture, Beltsville / USA), who was of great help for large parts of this thesis. My sincere
thanks are for letting me benefit from his outstanding knowledge on the biology and
diversity of water lilies. I am grateful to Prof. Klaus Peter Sauer and Prof. Thomas Litt (both
University of Bonn), as well as to all other members of the Graduiertenkolleg for sharing
their experience and for many stimulating discussions. Many thanks are due to Prof. Khidir
W. Hilu (Virginia Tech, Blacksburg / USA) for valuable suggestions on the outline of this
project.
The molecular data sets in this thesis were produced in the Molecular Systematics Lab at the
Nees Institute for Biodiversity of Plants in Bonn, which is led by Dr. Thomas Borsch. I wish
to express my warmest thanks to all my colleagues: Dr. Kai Müller, Andreas Worberg, Dr.
Dietmar Quandt, Dr. Rolf Blöcher, Kim Govers and Kassahun Tesfaye – thank you for all the
assistance in the lab and at the PC, for interesting discussions and for much sympathy. The
comments and suggestions of Kai Müller and Dietmar Quandt with regard to molecular
IV
evolution were especially helpful for the first part of my thesis. The respective chapter (2)
profited also a lot from discussions with Prof. Volker Knoop (University of Bonn), Dr. Scot
Kelchner (Idaho State University, Pocatello / USA) and Dr. Helga Ochoterena Booth
(Universidad Nacional Autónoma de México).
With regard to chapters 3 and 4, I am indebted to Dr. John Wiersema, Dr. Barre Hellquist
(Massachusetts College of Liberal Arts, North Adams / USA) and Dr. Surrey Jacobs (Royal
Botanical Gardens Sydney / Australia) for providing DNA material of several specimens of
Nymphaea and Ondinea and for extremely useful comments on the results of the
phylogenetic analyses. At this point I would also like to express my thanks to the Botanic
Gardens of Bonn University, especially to Dr. Wolfram Lobin and to Michael Neumann, for
curating and cultivating the living collection of water lilies, which was mainly established
through collections of Dr. Thomas Borsch.
The most integrative section of the present thesis is the last chapter, drawing a bow from
phylogeny and extant distribution to the fossil record and biogeographic history. Therefore, I
am indebted to many people who contributed to the completion of this part of the study.
First, I would like to mention the BIOMAPS group of the Nees Institute, namely Dr. Jens
Mutke, Holger Kreft, Dr. Wolfgang Küper and Henning Sommer. I could benefit a lot from
their practical know-how in geographic information systems and from the long–standing
experience and theoretical background in biodiversity mapping in this working group. I am
also very grateful to PD Dr. Volker Wilde (Forschungsinstitut Senckenberg, Frankfurt /
Germany), who shared his knowledge on earth history and the fossil record with me and
provided valuable suggestions for the interpretation of the data. This last chapter of my thesis
is an outcome of a close cooperation with Mi-Jeong Yoo (Soltis Lab, Florida Museum of
Natural History / USA). Mi-Jeong Yoo has conducted most of the work on molecular dating
of the Nymphaeales data set. I am very grateful to her for all the help, for the stimulating
discussions and the introduction into cloning methods – but also for the good time I had
during my stay at the Soltis Lab in Gainesville. I also sincerely thank Dr. Pamela Soltis and
Prof. Douglas Soltis for their valuable suggestions, the encouraging support and their warm
hospitality. Many thanks to Nils Köster, Holger Kreft, Nadja Korotkova and Andreas Worberg
(all University of Bonn) for proof–reading.
Last but not least I would like to express my deep gratitude to Dr. Tom Motzer for his
untiring personal encouragement and loving support. Thanks for being there and for standing
behind me. I very much enjoyed the time with you.
Contents

1 General Introduction 1
1.1 Why work on basal angiosperms?............................................................................2
1.2 Hypotheses on the evolution and phylogeny of basal angiosperms.........................5
1.2.1 The origin and early diversification of angiosperms.....................................5
1.2.2 Pre–cladistic hypotheses on angiosperm diversification...............................8
1.2.3 Cladistic analyses and the changing view on angiosperm relationships.......9
1.2.4 Current understanding of phylogenetic relationships.................................10
1.3 The age of angiosperms.........................................................................................12
1.3.1 Evidence from the fossil record..................................................................12
1.3.2 Insights from molecular studies..................................................................14
1.4 Extant and historical biogeography of basal angiosperms.......................................15
1.5 Nymphaeales — the first globally diverse clade of angiosperms............................17
1.6 Aims of the study and project design.....................................................................20
2 Phylogeny of basal angiosperms based on the petD group II intron 23
2.1 Introduction...........................................................................................................24
2.2 Materials and Methods...........................................................................................26
2.2.1 Taxon sampling and plant material............................................................26
2.2.2 DNA isolation............................................................................................26
2.2.3 Primer design.............................................................................................26
2.2.4 Amplification and sequencing....................................................................29
2.2.5 Sequence alignment...................................................................................29
2.2.6 Coding of length mutational events............................................................31
2.2.7 Secondary structure....................................................................................33
2.2.8 Phylogenetic analysis.................................................................................33
2.3 Results...................................................................................................................35
2.3.1 Overall sequence variability.......................................................................35
2.3.2 Microstructural changes.............................................................................36
2.3.3 Secondary structure....................................................................................37
2.3.4 Trees obtained from individual and combined data partitions....................40
VI
2.4 Discussion.............................................................................................................42
2.4.1 Sequence variability within the petD region..............................................42
2.4.2 Kind and distribution of length mutations..................................................42
2.4.3 Structural effects on sequence evolution in the group II intron..................42
2.4.4 Molecular evolution of the spacer..............................................................46
2.4.5 Phylogenetic signal of petD sequence data................................................46
2.4.6 Phylogeny of basal angiosperms................................................................48
2.5 Conclusion............................................................................................................48
3 Phylogenetic analysis of Nymphaeales using fast–evolving
and non–coding chloroplast markers 51
3.1 Introduction...........................................................................................................52
3.2 Materials and Methods..........................................................................................54
3.2.1 Taxon sampling and plant material............................................................54
3.2.2 DNA isolation, amplification and sequencing............................................57
3.2.3 Sequence alignment and indel coding.......................................................58
3.2.4 Phylogenetic analyses................................................................................58
3.3 Results...................................................................................................................60
3.3.1 Sequence variability observed in the data sets...........................................60
3.3.2 Trees obtained from different approaches..................................................62
3.3.3 Phylogeny of Nymphaeales.......................................................................66
3.3.4 Effects of taxon sampling...........................................................................66
3.4 Discussion.............................................................................................................68
3.4.1 Structure of data and reliability of the trees................................................68
3.4.2 Phylogeny and evolution of Nymphaeales.................................................70
3.4.3 Taxon sampling.........................................................................................73
3.4.4 Morphological characters in Nymphaeales................................................74
3.4.5 Phylogenetic signal of data partitions.........................................................74
4 Phylogenetic relationships among Australian water lilies
(Nymphaea subg. Anecphya) 77
4.1 Introduction...........................................................................................................78
4.2 Materials and Methods..........................................................................................80
4.2.1 Taxon sampling and plant material............................................................80
4.2.2 DNA isolation, amplification and sequencing............................................80
4.2.3 Sequence alignment and phylogenetic analysis.........................................85
4.2.4 Biogeographic data....................................................................................85
4.3 Results...................................................................................................................86
4.3.1 Sequence variability in ITS.........................................................................86
4.3.2 Sequence variability of the trnT–trnF region..............................................89
VII
4.3.3 Trees obtained from nuclear ITS sequences...............................................90
4.3.4 Trees obtained from the plastid marker trnT–trnF.......................................94
4.4 Discussion.............................................................................................................98
4.4.1 Sequence variability and phylogenetic utility of trnT–trnF
and ITS in Anecphya..................................................................................98
4.4.2 Polymorphic sites and incongruent trees provide evidence
for reticulate evolution...............................................................................99
4.4.3 Phylogenetic relationships and reticulate evolution in
Nymphaea subg. Anecphya.....................................................................102
4.4.4 The position of Ondinea purpurea...........................................................105
4.5 Conclusions and suggestions for further studies...................................................107
5 Biogeography of Nymphaeales: Extant patterns and historical events 109
5.1 Introduction.........................................................................................................110
5.1.1 Phylogeny and evolution of Nymphaeales...............................................111
5.1.2 The fossil record of Nymphaeales............................................................112
5.1.3 Geological settings...................................................................................114
5.1.4 Aims of this study.....................................................................................117
5.2 Materials and Methods.........................................................................................117
5.2.1 Taxon sampling and phylogenetic hypotheses.........................................117
5.2.2 Estimation of divergence times.................................................................118
5.2.3 Extant and fossil distribution....................................................................119
5.2.4 Dispersal–vicariance analysis...................................................................120
5.3 Results.................................................................................................................122
5.3.1 Extant distribution....................................................................................122
5.3.2 Estimated divergence times......................................................................126
5.3.3 Inferred ancestral areas.............................................................................127
5.4 Discussion...........................................................................................................132
5.4.1 Extant patterns of biodiversity in Nymphaeales........................................132
5.4.2 Divergence times in Nymphaeales and Nymphaeaceae...........................133
5.4.3 Ancestral areas and implications for possible dispersal scenarios.............135
5.4.4 Historical biogeography of Nymphaeales — a synthesis...........................136
5.5 Conclusion and prospect.....................................................................................144

Summary 147

References 149

List of Abbreviations 175

List of Figures 177

List of Tables 179

Appendix 181
VIII